Based on those variables you choose a CoC that suits you. After you have chosen the CoC you can then vary aperture, focal lenth and subject distance to estimate DOF.

There are standard CoC values that were traditionally chosen for 35mm film, enlarged to 8x12, for a viewer 1m from the print of average visual acuity. -> this is the value you get from the standard dropdown list on DOFMaster.

In the world of pixel peeping and large prints, Fuji have chosen a pretty conservative CoC which suggests that people will be printing larger and viewing closer (or looking at 1:1 zooms in photoshop, etc.)

Many of us have long felt that it would be very good for Fuji to allow in the menu settings a range of CoC choices which would then be reflected in the visible DOF scales.

For myself, I find the Fuji scales slightly too conservative, but the standard scales too relaxed. I would prefer to choose a setting in the middle.